Bob does not broadcast the refund at start as it would not be included to the block chain or mem pool until its time has come.
The point of micropayment channell is not to broadcast anything but the final version of the settlement transaction.
The payee can flush the latest version of the settlement transaction any time to the block chain which then double spends and thereby invalidates
the refund. If this happens long before the refund timeout then malleability is not a concern.
The payer signs new versions of the settlement transaction and sends them to payee. Payer can not broadcast them as they are only signed by payer.
The payee will sign and broadcast the most favorable to him and that is the regular close of the channel.
What prevents the payer (bob) from spending the bond before the settlement? If it is not on the network?
When you say settlement transaction? You mean the two separate transactions, bond and final refund? You mean to say that they are both broadcast at the same time at the 'end of work day'?
The payer signs new versions of the settlement transaction and sends them to payee. Payer can not broadcast them as they are only signed by payer.
After payer (bob) signs the bond, what prevents Payee (Alice) Spending the bond therefore invalidating refund? The way I understand it if the inputs of a time-locked transaction (refund) are spent before time elapses the time-locked transaction is invalid.